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XLConnect on Linux Mint Maya

9 messages · John McKown, kw1958, Jeff Newmiller +2 more

Original
Keith S Weintraub
# 
Folks,

I have been trying to get XLConnect to work on my Linux Mint Maya machine.

R works fine but this package doesn't seem to want to build. Here is the message I get after supposedly building XLConnect and rJava:
I purged the openJDK and downloaded the 1.7.0_65 JDK form Oracle.

The build and the compile seemed to work ok as there were no errors. For example I can generate ggplot2 graphs.

I know this is probably the wrong forum but if someone could gently point me in the right direction I would be very appreciative.

Thanks so much for your time,
KW



--
John McKown
#
On Thu, Jul 24, 2014 at 8:36 PM, Keith S Weintraub <kw1958 at gmail.com> wrote:
It works fine for me on Fedora 20 (and 19 before it). When I installed
R, it installed into /usr/lib64/R. There exists a file:
/usr/lib64/R/etc/ldpaths which is executed by the R executable script.
This sets up the LD_LIBRARY_PATH to point to the Java installation on
my machine. In the /usr/lib64/R/bin directory, there is a program
called "javareconf". I would suggest that you run this with the -n
switch, like:

R CMD /usr/lib64/R/bin/javareconf -n

This will show you what it _would_ do if you left off the "-n". Make
sure it looks reasonable. If it does, then run the same command,
without the "-n", as the "root" superuser. In my case, that would be:

sudo R CMD /usr/lib64/R/bin/javareconf

You need to be "root" because it update the file
/usr/lib64/R/etc/ldpaths . I am fairly sure this will fix your
problem.

===

As a possible alternative to XLConnect, have you looked at openxlsx?
It appears to have the same abilities, just some different syntax. It
says that it is written in C and so should be faster than XLConnect. I
have tested both packages, a little, and they both seem to work well.

Well, it's 22:14 hours here and I wish that I could fall asleep. We're
having problems at work and I know that the "big boss" will blame us
peons if the hardware isn't fixed promptly Despite the fact that we
are only software people and aren't allowed to touch the hardware. Our
management's minds are not using the same logic as mine does.
Frustrating.
4 days later
Keith S Weintraub
# 
John Et Al.

I can get rJava and XLConnect to work only if I run as super user.

Note that I have built rJava and XLConnect as super user (otherwise neither package works).


____________________________________________
Without sudo
Loading required package: XLConnect
Error : .onLoad failed in loadNamespace() for 'rJava', details:
  call: dyn.load(file, DLLpath = DLLpath, ...)
  error: unable to load shared object '/home/refserv/R/i686-pc-linux-gnu-library/3.1/rJava/libs/rJava.so':
  libjvm.so: cannot open shared object file: No such file or directory
_____________________________________________
With sudo

 > require(XLConnect)
Loading required package: XLConnect
XLConnect 0.2-7 by Mirai Solutions GmbH
http://www.mirai-solutions.com ,
http://miraisolutions.wordpress.com

______________________________________________
Note that I have changed the ownership (recursively) for rJava and XLConnect because they were previously owned by root. Also note that ggplot2 (included for comparison) was installed the usual way with no problem.

drwxr-xr-x 11 refserv refserv 4096 Jul 24 14:07 ggplot2/
drwxr-xr-x 10 refserv refserv 4096 Jul 29 08:28 rJava/
drwxr-xr-x 11 refserv refserv 4096 Jul 29 10:09 XLConnect/

________________________________________________

Despite "no such file or directory" above:

/home/refserv/R/i686-pc-linux-gnu-library/3.1/rJava $ ls -altr /home/refserv/>
-rwxr-xr-x 1 refserv refserv 273489 Jul 29 08:28 /home/refserv/R/i686-pc-linux-gnu-library/3.1/rJava/libs/rJava.so

The file rJava.so exists.

Thanks so much for your time and help,
Best,
KW

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On Jul 24, 2014, at 11:16 PM, John McKown <john.archie.mckown at gmail.com> wrote:

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Jeff Newmiller
    

    

      
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Sounds to me like a problem outside of R (off topic here). In particular, it doesn't sound like you are using the appropriate tools (apt-get package manager for R and a JDK; R install.package() for your R packages) to admin your machine. The only thing you should need sudo for is to run apt-get... everything else should be done as a normal user unless you really know what you are doing. I had no problem installing it just now on my Ubuntu machine with OpenJDK. I have no experience with Mint but Google tells me you should be able to use the instructions for Ubuntu... I would expect Google to tell you the same thing if you ask nicely... your most challenging task at this point should be cleaning up the mess you have made by excessive use of sudo ... most likely running R with it (only update your personal R library directories so you are not tempted to go rogue) but you don't say how you installed the jdk so that could also be messed up. 
---------------------------------------------------------------------------
Jeff Newmiller                        The     .....       .....  Go Live...
DCN:<jdnewmil at dcn.davis.ca.us>        Basics: ##.#.       ##.#.  Live Go...
                                      Live:   OO#.. Dead: OO#..  Playing
Research Engineer (Solar/Batteries            O.O#.       #.O#.  with
/Software/Embedded Controllers)               .OO#.       .OO#.  rocks...1k
--------------------------------------------------------------------------- 
Sent from my phone. Please excuse my brevity.

        
On July 29, 2014 8:19:33 AM PDT, Keith S Weintraub <kw1958 at gmail.com> wrote:

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Ista Zahn
    

    

      
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On Tue, Jul 29, 2014 at 12:54 PM, Jeff Newmiller

        
<jdnewmil at dcn.davis.ca.us> wrote:

            

      
      
      
    

        
Possibly, but I suspect that the OP now has two versions of XLConnect
installed, one in the user R library and one in the system-wide R
library.

Keith, try

remove.packages("XLConnect")
remove.packages("rJava")

WITHOUT sudo. Then restart R; you should now get the (working)
system-wide versions of rJava and XLConnect.

HTH,
Ista

 In particular, it doesn't sound like you are using the appropriate
tools (apt-get package manager for R and a JDK; R install.package()
for your R packages) to admin your machine. The only thing you should
need sudo for is to run apt-get... everything else should be done as a
normal user unless you really know what you are doing. I had no
problem installing it just now on my Ubuntu machine with OpenJDK. I
have no experience with Mint but Google tells me you should be able to
use the instructions for Ubuntu... I would expect Google to tell you
the same thing if you ask nicely... your most challenging task at this
point should be cleaning up the mess you have made by excessive use of
sudo ... most likely running R with it (only update your personal R
library directories so you are not tempted to go rogue) but you don't
say how you installed the jdk so that could also be messed up.

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    
1 day later

    

      
      

        


  

        

      Keith S Weintraub
    

    

      
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Ista Et Al,
Unfortunately your suggestion to use remove.packages did exactly the reverse of what you thought would happen.

I have cleaned up my installation but still have trouble getting rJava to install properly and of course that means that XLConnect cannot install either.

-------------------------------------
I think this shows that the java-7-openjdk is working.
-------------------------------------
/home/refserv $ sudo R CMD javareconf
Java interpreter : /usr/bin/java
Java version     : 1.7.0_55
Java home path   : /usr/lib/jvm/java-7-openjdk-i386/jre
Java compiler    : /usr/bin/javac
Java headers gen.: /usr/bin/javah
Java archive tool: /usr/bin/jar

trying to compile and link a JNI progam 
detected JNI cpp flags    : -I$(JAVA_HOME)/../include
detected JNI linker flags : -L$(JAVA_HOME)/lib/i386/client -ljvm
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/lib/jvm/java-7-openjdk-i386/jre/../include     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c conftest.c -o conftest.o
gcc -std=gnu99 -shared -Wl,-Bsymbolic-functions -Wl,-z,relro -o conftest.so conftest.o -L/usr/lib/jvm/java-7-openjdk-i386/jre/lib/i386/client -ljvm -L/usr/lib/R/lib -lR


JAVA_HOME        : /usr/lib/jvm/java-7-openjdk-i386/jre
Java library path: $(JAVA_HOME)/lib/i386/client
JNI cpp flags    : -I$(JAVA_HOME)/../include
JNI linker flags : -L$(JAVA_HOME)/lib/i386/client -ljvm
Updating Java configuration in /usr/lib/R
Done.
___________________________________


-------------------------------------
Purge and re-install rjava
-------------------------------------
/home/refserv $ sudo apt-get --purge remove r-cran-rjava
Reading package lists... Done
Building dependency tree       
Reading state information... Done
The following packages will be REMOVED:
  r-cran-rjava*
0 upgraded, 0 newly installed, 1 to remove and 3 not upgraded.
After this operation, 1,651 kB disk space will be freed.
Do you want to continue [Y/n]? y
(Reading database ... 173764 files and directories currently installed.)
Removing r-cran-rjava ...

/home/refserv $ sudo apt-get install r-cran-rjava       
Reading package lists... Done
Building dependency tree       
Reading state information... Done
The following NEW packages will be installed:
  r-cran-rjava
0 upgraded, 1 newly installed, 0 to remove and 3 not upgraded.
Need to get 0 B/557 kB of archives.
After this operation, 1,651 kB of additional disk space will be used.
Selecting previously unselected package r-cran-rjava.
(Reading database ... 173625 files and directories currently installed.)
Unpacking r-cran-rjava (from .../r-cran-rjava_0.9-3-1_i386.deb) ...
Setting up r-cran-rjava (0.9-3-1) ...
-------------------------------------
-------------------------------------



-------------------------------------
Here I try to install rJava in R 
but it looks like there is a version problem.

Given I am using openjdk above I am not sure why R is looking at the oracle Java
-------------------------------------

home/refserv $ R

R version 3.1.1 (2014-07-10) -- "Sock it to Me"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: i686-pc-linux-gnu (32-bit)

........................................ (just cutting down on the output)

            

      
      
      
    

        
Loading required package: rJava
Failed with error:  ?package ?rJava? was built before R 3.0.0: please re-install it?

            

      
      
      
    

        
Installing package into ?/home/refserv/R/i686-pc-linux-gnu-library/3.1?
(as ?lib? is unspecified)
--- Please select a CRAN mirror for use in this session ---
trying URL 'http://cran.mirrors.hoobly.com/src/contrib/rJava_0.9-6.tar.gz'
Content type 'application/x-gzip' length 567515 bytes (554 Kb)
opened URL
==================================================
downloaded 554 Kb


........................................ (just cutting down on the output)


checking Java support in R... present:
interpreter : '/usr/lib/jvm/java-7-oracle/jre/bin/java'
archiver    : '/usr/lib/jvm/java-7-oracle/bin/jar'
compiler    : '/usr/lib/jvm/java-7-oracle/bin/javac'
header prep.: '/usr/lib/jvm/java-7-oracle/bin/javah'
cpp flags   : '-I/usr/lib/jvm/java-7-oracle/include -I/usr/lib/jvm/java-7-oracle/include/linux'
java libs   : '-L/usr/lib/jvm/java-7-oracle/jre/lib/i386/client -ljvm'
checking whether Java run-time works... ./configure: line 3729: /usr/lib/jvm/java-7-oracle/jre/bin/java: No such file or directory
no
configure: error: Java interpreter '/usr/lib/jvm/java-7-oracle/jre/bin/java' does not work
ERROR: configuration failed for package ?rJava?
* removing ?/home/refserv/R/i686-pc-linux-gnu-library/3.1/rJava?

The downloaded source packages are in
	?/tmp/RtmpwvY4Md/downloaded_packages?
Warning message:
In install.packages("rJava") :
  installation of package ?rJava? had non-zero exit status

-------------------------------------
-------------------------------------

Thanks again for your time,
Best,
KW


--

        
On Jul 29, 2014, at 2:22 PM, Ista Zahn <istazahn at gmail.com> wrote:

        

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Ista Zahn
    

    

      
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Hi Keith,

So the plot thickens. How is it that you have R 3.1.1 but apt-get
install rJava gives you an old version of the package? This may be
potentially difficult to figure out, but you can try some easy things
first. If I were you I would start with

sudo apt-get remove r-base r-devel
sudo apt-get update
sudo apt-get dist-upgrade
sudo apt-get install r-base r-devel r-cran-rjava
sudo R CM D javareconf


Then restart the computer. Or something like that.

Finally, note that there is a specific mailing list for those running
R on debian (of which mint is a (n indirect) derivative): see
https://stat.ethz.ch/mailman/listinfo/r-sig-debian. You may have
better luck asking your question there.

Best,
Ista

        
On Thu, Jul 31, 2014 at 8:46 AM, Keith S Weintraub <kw1958 at gmail.com> wrote:

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Keith S Weintraub
    

    

      
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Thanks Ista,
I will try your procedure next Tuesday. This is going pretty slow because I only work at that machine Tuesday-Thursday.

I will let you know how it goes (lucky you!) by private email as I don't think there is any use in bothering all of r-help.

After trying your suggestions next week I will switch over to the r-sig-debian group and start bothering them.

Thanks again for everyone that chimed in to help me,
Best,
KW

--

        
On Jul 31, 2014, at 2:54 PM, Ista Zahn <istazahn at gmail.com> wrote: